Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

Authors: LIU, ZHANJIANG - Auburn University; Leeds, Timothy - Tim; Vallejo, Roger; Bosworth, Brian; Waldbieser, Geoffrey - Geoff; Palti, Yniv; Beck, Benjamin; Shoemaker, Craig; Blackburn, Harvey; Rexroad, Caird; Proestou, Dina

Submitted to: BMC Genomics
Publication Type: Other
Publication Acceptance Date: 2/3/2017
Publication Date: 2/21/2017
Publication URL: https://handle.nal.usda.gov/10113/5642525
Citation: Liu, Z., Leeds, T.D., Vallejo, R.L., Bosworth, B.G., Waldbieser, G.C., Palti, Y., Beck, B.H., Shoemaker, C.A., Blackburn, H.D., Rexroad III, C.E., Proestou, D.A. 2017. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. Biomed Central (BMC) Genomics. 18:191. doi:10.1186/s12864-017-3557-1.

Interpretive Summary:

Technical Abstract: The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic variations and relationship with phenotypic variations. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.